Resgrp:comp-photo-hpc-ax1

IC has several centrally-managed HPC computer systems: mainly we use the PC cluster CX1.

AX1 & AX2 obsolete: AX3 replacement to follow, which shares CX1 binaries.

--Mjbear 10:51, 22 September 2011 (BST)

But there is also a small Silicon Graphics AX1. This and an older separate machine AX2 (added as an AX1 queue) are soon to be replaced, but they are still useful for larger shared memory parallel calculations. (No Linda parallelism - just one large 'node' each.)

Filesystems such as $HOME and $WORK are shared with CX1. For AX1 (AX2) need to use versions of Gaussian compiled specifically for Silicon Graphics.

--Mjbear 11:15, 23 March 2011 (UTC) (update)

Connecting

To connect to AX1 and forward display information for X-windows, use

ssh -Y myaccount@login.ax1.hpc.ic.ac.uk

Use your IC college account.

Don't log in to AX2 directly.

Queuing system

The Silicon Graphics uses the PBS queueing system, as CX1 does. One difference: qstat appears to list all calculations queued.

To run calculations on AX2, use e.g.

#PBS -q ax2
#PBS -l walltime=71:59:00
#PBS -l mem=10000mb
#PBS -l ncpus=8
#PBS -joe

in your jobscript, to specify the ax2 queue.

Gaussian

Default Gaussian version for SGI is accessible via

module load gaussian

The development version installed is gdv h01, accessible via

module load gaussian/devel-modules
module load gdvh01_ax1

This has been built for ia64/SGI, but not tested extensively yet. Some problems encountered with memory exceptions, suggesting we haven't got the build options right yet.

h01 is not the latest devel release.

Building Gaussian

I used the following in my .cshrc:

setenv gdvroot "/home/gaussian-devel/gaussiandvh01_ax1"
module load intel-suite/10.0

This gives the supported versions of the Intel compilers (10.0.023) & MKL library (9.1.018) for Gaussian.

Built using

nohup bldgdv all ia64 >& bldgdv_all_ia64_gdvh01_ax1.log & 

(gau-machine gives ia64 correctly, so $2 is redundant)

Libraries are not in the default location, so ia64.make was patched:

ia64.make:#MKLLIB = /opt/intel/ilp64
ia64.make:MKLLIB = /opt/intel/mkl/9.1/lib/64
ia64.make:BLAS = $(MKLLIB)/libmkl_ipf.a

To Do: use $MKL_HOME for /apps/intel/mkl/9.1.018/, which will be compatible with later versions.

Development links

An example makefile for a development link - hardwired for intel-suite/10.0 - is in

/home/gaussian-devel/gaussiandvh01_ax1/gdvtest_502